Protein Dynamics: Methods and Protocols

Geometric simulation of flexible motion in proteins
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  • Protein Dynamics
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  • Protein Dynamics : Methods and Protocols - giuliettasprint.konfer.eu
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  • Protein Dynamics : Methods and Protocols

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    Description In Protein Dynamics: Methods and Protocols, expert researchers in the field detail both experimental and computational methods to interrogate molecular level fluctuations. Chapters detail best-practice recipes covering both experimental and computational techniques, reflecting modern protein research. Written in the highly successful Methods in Molecular Biology TM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.

    Authoritative and practical, Protein Dynamics: Methods and Protocols describes the most common and powerful methods used to characterize protein dynamics. Other books in this series. Hemostasis and Thrombosis Emmanuel J. Add to basket. Cancer Cytogenetics Thomas S. Immunogenetics Frank T. Natural Products Isolation Satyajit D.

    Protein Dynamics

    Surface Plasmon Resonance Nico J. Plant Pathology Christophe Lacomme. Marine Genomics Sarah J. Metabolic Flux Analysis Jens O. Vaccinia Virus Jason Mercer. Recurrence plots of dynamical systems. Europhys Lett. Marwan N. A historical review of recurrence plots.

    Protein Dynamics: Methods and Protocols (Methods in Molecular Biology)

    Eur Phys J-Spec Top. Recurrence plots for the analysis of complex systems. Phys Rep. Dynamical assessment of physiological systems and states using recurrence plot strategies.

    • Protein Dynamics: Methods and Protocols - Google книги!
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    • Morphing Methods to Visualize Coarse-Grained Protein Dynamics?
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    • Confocal single-molecule FRET for protein conformational dynamics?
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    J Appl Physiol. Giuliani A, Manetti C. Hidden peculiarities in the potential energy time series of a tripeptide highlighted by a recurrence plot analysis: a molecular dynamics simulation.

    Phys Rev E. JP Zbilut. Recurrence quantification analysis as a tool for characterization of molecular dynamics simulations. Nonlinear methods in the analysis of protein sequences: a case study in rubredoxins. Biophys J. The role of hydrophobicity patterns in prion folding as revealed by recurrence quantification analysis of primary structure. Protein Eng. Mapping protein sequence spaces by recurrence quantification analysis: a case study on chimeric structures. A complexity score derived from principal components analysis of nonlinear order measures.

    Physica A: Stat Mech Appl. Elucidating protein secondary structures using alpha-carbon recurrence quantifications. Recurrence analysis of hydration effects on nonlinear protein dynamics: multiplicative scaling and additive processes. Phys Lett A. Nonlinear signal analysis methods in the elucidation of protein sequence-structure relationships. Chem Rev-Columbus. Review of nonlinear analysis of proteins through recurrence quantification.

    Cell Biochem Biophys. Giuliani A, Tomasi M. Recurrence quantification analysis reveals interaction partners in paramyxoviridae envelope glycoproteins.

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    Large contact surface interactions between proteins detected by time series analysis methods: case study on C-phycocyanins. Charge and hydrophobicity patterning along the sequence predicts the folding mechanism and aggregation of proteins: a computational approach. J Proteome Res. Discrimination of single amino acid mutations of the p53 protein by means of deterministic singularities of recurrence quantification analysis. Nonlinear analysis of sequence symmetry of beta-trefoil family proteins.

    Chaos, Solitons Fractals. Nonlinear correlations of protein sequences and symmetries of their structures. Chin Phys Lett. Structure-related statistical singularities along protein sequences: a correlation study.

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    J Biomol Struct Dyn. Distribution of three a and all five b SCOP classes colors onto partitionings of the dynasome 1…5 obtained from k-means clustering. References Publications referenced by this paper. The delay parameter. Majestic Books London, ,, United Kingdom. Eigenvalues are given as fractions of the sum of all eigenvalues.

    J Chem Inf Model. Entropic criteria for protein folding derived from recurrences: six residues patch as the basic protein word. FEBS Lett.

    Protein Dynamics : Methods and Protocols - giuliettasprint.konfer.eu

    Predicting alternate structure attainment and amyloidogenesis: a nonlinear signal analysis approach. Biochem Biophys Res Commun. Nonlinear analysis of sequence repeats of multi-domain proteins. Cluster protein structures using recurrence quantification analysis on coordinates of alpha-carbon atoms of proteins.

    Using recurrence quantification analysis descriptors for protein sequence classification with support vector machines. J Biomol Struct Dyn. System dynamics revealed by recurrence quantification analysis: application to molecular dynamics simulations. Proteins as networks: usefulness of graph theory in protein science. Curr Protein Pept Sci.

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    Implications from a network-based topological analysis of ubiquitin unfolding simulations. PLoS One. Angadi S, Kulkarni A. Nonlinear signal analysis to understand the dynamics of the protein sequences. Remote protein homology detection using recurrence quantification analysis and amino acid physicochemical properties. J Theor Biol. Identification of Defensins employing recurrence quantification analysis and random Forest classifiers.

    Pattern Recognition and Machine Intelligence. Prediction of protein structural classes by recurrence quantification analysis based on chaos game representation. Application of recurrence quantification analysis RQA in biosequence pattern recognition. Adv Comput Commun. Analysis of intrinsically disordered regions in proteins using recurrence quantification analysis.

    Inter J Bifurcation Chaos. Predicting the subcellular location of apoptosis proteins based on recurrence quantification analysis and the Hilbert-Huang transform. Chinese Physics B. Looking for a sequence based allostery definition: a statistical journey at different resolution scales.

    Protein Dynamics : Methods and Protocols

    Shao G, Yuehui C. Predict the tertiary structure of protein with flexible neural tree. Intell Comput Theories App. The adaptive nature of protein residue networks.

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    Karain WI. THz frequency spectrum of protein—solvent interaction energy using a recurrence plot-based Wiener—Khinchin method. Weighted protein residue networks based on joint recurrences between residues. BMC bioinformatics. Fataftah H, Karain WI. Detecting protein atom correlations using correlation of probability of recurrence.

    Takens F.